Sent to CCL by: "JAMES VIVIAN" [jamestvivian++msn.com] Don:You're basically correct that at the conceptual & mathematical level, things are pretty straightforward; you need to create & store ~3*N coordinates for N particles, and F=ma tells the story. So you then need an integrator. And a force-field. And maybe a linked-list (Verlet), and some trickerly for periodic-boundary conditions, etc.. But the core or heart of the MD simulation remains a fairly brief chunk of code, much like the engine in a car is a relatively small fraction of the whole beast.
Once you factor in the GUI, the flexibility to elect different ensembles (NVT, NPT, uVT Grand Canonical...), different force field / energetic options, solvation, build in constraints, SHAKE, RATTLE, thermostats, etc., then things tend to spawn. So to craft a generally multi-purpose MD package, things tend to get unwieldly in a hurry. And a lot of packages don't just stop at generating trajectories; they'll allow you to do some degree of post-processing, maybe even allow you to evaluate a time correlation function, etc..
So they end up being non-trivial and worth the $$$ when you assemble all the pieces in a shrink-wrapped package.
From: "Don Steiger sd00_2002::yahoo.com" <owner-chemistry : ccl.net> Reply-To: "CCL Subscribers" <chemistry : ccl.net> To: "Vivian, James T " <jamestvivian : msn.com> Subject: CCL: MD software question. Date: Sat, 28 Jan 2006 20:51:09 -0500 Sent to CCL by: "Don Steiger" [sd00_2002[-]yahoo.com]I have an MD question. As far as I can tell, the equations/math that goes into MD are fairly straight forward and short. Yet there are a lot of MD packages, and all of them are very large. So what is in these packages that makes them so large?>